A statistical model for antibody-antigen binding

We discuss a statistical model for antibody-antigen binding. The two macromolecules are assumed to be linked by a number of relatively weak bonds (or groups of correlated bonds) that are assumed to open and close statistically. We use the model for a preliminary analysis of experiments performed in the Institute of Biophysics at the Johannes Kepler University. In these experiments the two molecules are brought into contact using an atomic force microscope; then a prescribed time dependent force is applied to the bond and the distribution of times needed to pull the molecules completely apart is measured. This quantity is calculated with our model; its dependence on the model parameters (binding free energies, number of groups of correlated elementary bonds, force dependence of the binding free energy) is determined.Обговорюється статистична модель, яка описує зв’язування антитіло-антиген. При цьому вважається, що дві макромолекули можуть поєднуватись через набір відносно слабих зв’язків (чи груп скорельованих зв’язків), що відкриваються і закриваються статистично. Ця модель використовується для попереднього аналізу експериментів, виконаних в Інституті біофізики Університету Йогана Кеплера. У цих експериментах дві молекули приводились у контакт, використовуючи атомної сили мікроскоп, а потім прикладалася певна залежна від часу сила до зв’язку і вимірювався розподіл часів, необхідних для повного розділення молекул. Ця характеристика розраховується з використанням запропонованої моделі; знайдена її залежність від модельних параметрів (вільних енергій зв’язування, числа груп скорельованих елементарних зв’язків, залежності вільної енергії зв’язування від сили)

Field-driven solid-on-solid interfaces moving under a stochastic Arrhenius dynamic: effects of the barrier height

We present analytical results and kinetic Monte Carlo simulations for the mobility and microscopic structure of solid-on-solid (SOS) interfaces driven far from equilibrium by an external force, such as an applied field or (electro)chemical potential difference. The interfaces evolve under a specific stochastic dynamic with a local energy barrier (an Arrhenius dynamic), known as the transition dynamics approximation (TDA). We calculate the average height of steps on the interface, the average interface velocity, and the skewness of the interface as functions of the driving force and the height of the energy barrier. We find that the microscopic interface structure depends quite strongly on the barrier height. As the barrier becomes higher, the local interface width decreases and the skewness increases, suggesting increasing short-range correlations between the step heights.Comment: 6 pages, 5 figs. RevTe

Deep learning-assisted radiomics facilitates multimodal prognostication for personalized treatment strategies in low-grade glioma

Determining the optimal course of treatment for low grade glioma (LGG) patients is challenging and frequently reliant on subjective judgment and limited scientific evidence. Our objective was to develop a comprehensive deep learning assisted radiomics model for assessing not only overall survival in LGG, but also the likelihood of future malignancy and glioma growth velocity. Thus, we retrospectively included 349 LGG patients to develop a prediction model using clinical, anatomical, and preoperative MRI data. Before performing radiomics analysis, a U2-model for glioma segmentation was utilized to prevent bias, yielding a mean whole tumor Dice score of 0.837. Overall survival and time to malignancy were estimated using Cox proportional hazard models. In a postoperative model, we derived a C-index of 0.82 (CI 0.79-0.86) for the training cohort over 10 years and 0.74 (Cl 0.64-0.84) for the test cohort. Preoperative models showed a C-index of 0.77 (Cl 0.73-0.82) for training and 0.67 (Cl 0.57-0.80) test sets. Our findings suggest that we can reliably predict the survival of a heterogeneous population of glioma patients in both preoperative and postoperative scenarios. Further, we demonstrate the utility of radiomics in predicting biological tumor activity, such as the time to malignancy and the LGG growth rate

Manipulation of polarisations for broadband terahertz waves emitted from laser plasma filaments

Polarization control of broadband terahertz waves is essential for applications in many areas such as material sciences, medical and biological diagnostics, near-field communications and public securities. Conventional methods for polarization control are limited to narrow bandwidth and often with low efficiency. Here based upon theoretical and experimental studies, we demonstrate that the two-colour laser scheme in gas plasma can provide effective control of elliptically polarized terahertz waves, including their ellipticity, azimuthal angle, and chirality. This is achieved with a circularly-polarized laser at the fundamental frequency and its linearly polarized second harmonic, a controlled phase difference between these two laser components, as well as a suitable length of the laser plasma filament. A flexible control of their ellipticity and azimuthal angle is demonstrated with our theoretical model and systematic experiments. This offers a unique and flexible technique on the polarization control of broadband terahertz radiation suitable for wide applications

Birefringence measurement in the THz range based on double Fourier analysis

This paper was published in Optics Letters and is made available as an electronic reprint with the permission of OSA. The paper can be found at the following URL on the OSA website: http://dx.doi.org/10.1364/OL.39.000809. Systematic or multiple reproduction or distribution to multiple locations via electronic or other means is prohibited and is subject to penalties under law"A method for obtaining the average refractive indexes of a birefringent material in the terahertz region in a single measurement with a standard terahertz time-domain spectrometer is presented. The method is based on processing the frequency-domain interference between terahertz pulses and echoes through the Fourier transform of the terahertz spectrum. The technique also allows the determination of the optical axis orientation of the material by making two measurements with different angles of the sample optical axis. (C) 2014 Optical Society of AmericaThe authors thank the Erasmus Mundus scholarship and the Consejo Nacional de Investigaciones Cientificas y Tecnicas (Conicet) that support the work of Federico Sanjuan at Universitat Politecnica de Valencia and the Spanish Ministerio de Economia y Competitividad for partially supporting this work through project TEC2012-35797. Federico Sanjuan also thanks Dr. Jorge Tocho for his encouragement and support.Sanjuan, F.; Bockelt, AS.; Vidal Rodriguez, B. (2014). Birefringence measurement in the THz range based on double Fourier analysis. Optics Letters. 39(4):809-812. https://doi.org/10.1364/OL.39.000809S809812394Wiesauer, K., & Jördens, C. (2013). Recent Advances in Birefringence Studies at THz Frequencies. Journal of Infrared, Millimeter, and Terahertz Waves, 34(11), 663-681. doi:10.1007/s10762-013-9976-4Jördens, C., Scheller, M., Wietzke, S., Romeike, D., Jansen, C., Zentgraf, T., … Koch, M. (2010). Terahertz spectroscopy to study the orientation of glass fibres in reinforced plastics. Composites Science and Technology, 70(3), 472-477. doi:10.1016/j.compscitech.2009.11.022Jördens, C., Scheller, M., Wichmann, M., Mikulics, M., Wiesauer, K., & Koch, M. (2009). Terahertz birefringence for orientation analysis. Applied Optics, 48(11), 2037. doi:10.1364/ao.48.002037Kim, Y., Yi, M., Kim, B. G., & Ahn, J. (2011). Investigation of THz birefringence measurement and calculation in Al_2O_3 and LiNbO_3. Applied Optics, 50(18), 2906. doi:10.1364/ao.50.002906Reid, M., & Fedosejevs, R. (2006). Terahertz birefringence and attenuation properties of wood and paper. Applied Optics, 45(12), 2766. doi:10.1364/ao.45.002766Katletz, S., Pfleger, M., Pühringer, H., Mikulics, M., Vieweg, N., Peters, O., … Wiesauer, K. (2012). Polarization sensitive terahertz imaging: detection of birefringence and optical axis. Optics Express, 20(21), 23025. doi:10.1364/oe.20.023025Duvillaret, L., Garet, F., & Coutaz, J.-L. (2000). Influence of noise on the characterization of materials by terahertz time-domain spectroscopy. Journal of the Optical Society of America B, 17(3), 452. doi:10.1364/josab.17.000452Grischkowsky, D., Keiding, S., van Exter, M., & Fattinger, C. (1990). Far-infrared time-domain spectroscopy with terahertz beams of dielectrics and semiconductors. Journal of the Optical Society of America B, 7(10), 2006. doi:10.1364/josab.7.00200

Force-Induced Lysozyme—HyHEL5 Antibody Dissociation and Its Analysis by Means of a Cooperative Binding Model

Dynamic force spectroscopy probes the kinetic properties of molecules interacting with each other such as antibody-antigen, receptor-ligand, etc. In this article, a statistical model for the dissociation of such cooperative systems is presented. The partner molecules are assumed to be linked by a number of relatively weak bonds that can be grouped together into cooperative units. Single bonds are assumed to open and close statistically. Our model was used to analyze molecular recognition experiments of single receptor-ligand pairs in which the two molecules are brought into contact using an atomic force microscope, which leads to the formation of a strong and specific bond. Then a prescribed time-dependent force is applied to the complex and the statistical distribution of forces needed to pull the molecules completely apart is measured. This quantity is also calculated from our model. Furthermore, its dependence on the model parameters, such as binding free energy, number of bonds and groups, number of cooperative elementary bonds and degree of cooperativity within a group, influence of the force on the binding free energy, and the rate of change of the pulling force, is determined